mobr

Measurement of Biodiversity in R

This reposititory hosts an R package that is being developed for estimating biodiversity and the components of its change.

The concepts and methods behind this R package are described in two preprints that are both currently in review.

McGlinn, D.J. X. Xiao, F. May, S. Blowes, J. Chase, N. Gotelli, T. Knight, B. McGill, and O. Purschke. preprint. MoB (Measurement of Biodiversity): a method to separate the scale-dependent effects of species abundance distribution, density, and aggregation on diversity change. bioRxiv 244103. doi: https://doi.org/10.1101/244103.

Chase, J.M., B. McGill, D.J. McGlinn, F. May, S.A. Blowes, X. Xiao, T. Knight. prepint. Embracing scale-dependence to achieve a deeper understanding of biodiversity and its change across communities. bioRxiv 275701. doi: https://doi.org/10.1101/275701

How to install mobr

The easiest option is to install the package directly from GitHub using the package devtools. If you do not already have devtools installed then need to install it.

install.packages('devtools')
library(devtools)

The package also requires the dplyr package which has many dependencies. If you do not already have the dplyr package installed we suggest you install it and all of its dependencies using :

install.packages(c('bindrcpp','glue','pkgconfig','tibble','plyr','dplyr'))

Then check that dplyr can be loaded with library(dplyr). Now you should be ready to go with the mobr install

install_github('MoBiodiv/mobr')

Examples

The package vignette provides a useful walkthrough the package tools, but below is some example code that uses the two key analyses and related graphics.

library(mobr)
data(inv_comm)
data(inv_plot_attr)
inv_mob_in = make_mob_in(inv_comm, inv_plot_attr)
inv_stats = get_mob_stats(inv_mob_in, 'group')
plot(inv_stats)
inv_deltaS = get_delta_stats(inv_mob_in, 'group', ref_group='uninvaded',
                              type='discrete', log_scale=TRUE)
plot(inv_deltaS, 'invaded', 'uninvaded')

How to contribute to this project

1. Fork the repo to your local GitHub account

2. Clone your forked version of the repo to your machine

git clone git@github.com:your_user_name/mobr.git

3. Link your local repo back to the master on MoBiodiv

git remote add upstream git@github.com:MoBiodiv/mobr.git

4. Create a branch for your changes

git branch new_function

5. Checkout your branch

git checkout new_function

6. Make your commits on that branch and when you are done push it to your forked copy of the repo

git push origin new_function

7. Submit a pull request on the GitHub website by going to your forked copy of the repo and clicking on the pull request button

8. After your changes are merged with master you'll want to merge that update to master with your copies as well.

git pull upstream master
git push origin master
# delete your branch as its no longer needed
git branch -d new_function

Before your start work on the project in the future you'll want to repeat step 8 so that your version of the repo does not become out-of-sync with the main repository.